[BioPython] blast

[Julien Cigar]

On Wed, 2008-07-23 at 15:18 +0100, Peter Cock wrote:
> > Thanks, I got another formula which seems to work well too (and which
> > seems cleaner than counting the number of '|') :
> >
> > float(100) * float(hsp.score) / float(alignment.length)
> 
> I don't think that gives you the same thing as the percentage identify
> (see my other email).
> 

Indeed..! (sorry I sended my last mail before reading yours).

> >> Have you considered actually showing the blast alignment too?
> >>
> > Yes, it's in the output, I just replaced the '|' with a red background
> > and the ' ' with a green background, so they see directly where it
> > doesn't match
> 
> Since the graphical representation of the match/mismatch string is
> done using the colours red and green, it is useless for anyone who is
> colour blind.
> 

You're right .. I haven't thought about this

> Also the user can't cut and paste the alignment into an email or other
> document (electronic lab book?), which seems like an obvious thing to
> want to do.
> 
> Personally, I would try and keep the output looking more similar to
> traditional blast, as then its easier to understand (assuming you
> already know BLAST!).
> 

ok, I'll ask them what they prefer.

> Peter

Thanks,
Julien

-- 
Julien Cigar
Belgian Biodiversity Platform
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